Yes I can confirm this. If you try to change only your prefs (at least as an admin) into Preferences->your pref->Email Preferences, It never wan't to register the settings. It works the first time, and forget them just after the first consultation (or trying to make a filter, etc ...).
I use both custom setup and not custom setup and it's fail.
I found no info into the phpgw_config table about the mail. Is this normal ? (I suppose that the mail put its config there)